[Bug] Plan mode exit and permission bypass drops /deepthink command execution

Bug Description
There was a bug where I was in Plan mode, asked claude to investigate deeper a topic with a personal skill (/deepthink) it said it had to quit plan mode to use the skill (??) and proposed to clear and bypass permissions. When I did so, it started the implementation. Completely droping the instructions to use deepthink

Environment Info

• Platform: darwin
• Terminal: ghostty
• Version: 2.1.29
• Feedback ID: 7f66f171-6a77-41d0-9c90-4a2925d24393

Errors

[{"error":"Error: Failed to initialize LSP server plugin:jdtls-lsp:jdtls: LSP server 'plugin:jdtls-lsp:jdtls': startupTimeout is not yet implemented. Remove this field from the configuration.\n    at _ (/$bunfs/root/claude:2142:32620)\n    at processTicksAndRejections (native:7:39)","timestamp":"2026-02-02T09:21:19.919Z"},{"error":"MaxFileReadTokenExceededError: File content (86209 tokens) exceeds maximum allowed tokens (25000). Please use offset and limit parameters to read specific portions of the file, or use the GrepTool to search for specific content.\n    at RVB (/$bunfs/root/claude:3523:5255)\n    at async call (/$bunfs/root/claude:3532:1511)\n    at async <anonymous> (/$bunfs/root/claude:3544:1608)\n    at processTicksAndRejections (native:7:39)","timestamp":"2026-02-02T09:28:59.235Z"},{"error":"Error: Request was aborted.\n    at makeRequest (/$bunfs/root/claude:360:3940)\n    at processTicksAndRejections (native:7:39)","timestamp":"2026-02-02T11:20:46.431Z"},{"error":"Error: Request was aborted.\n    at makeRequest (/$bunfs/root/claude:360:3940)\n    at processTicksAndRejections (native:7:39)","timestamp":"2026-02-02T11:21:01.700Z"},{"error":"Error: Command failed: /opt/homebrew/Caskroom/claude-code/2.1.29/claude --ripgrep --files --glob frontend/features/taxonomy/lib/*.ts --sort=modified --no-ignore --hidden /Users/widgethiro/.ccswitch/worktrees/monorepo/pivot-24868/frontend\n    at genericNodeError (node:child_process:998:22)\n    at exitHandler (node:child_process:103:28)\n    at emit (node:events:98:22)\n    at #maybeClose (node:child_process:766:16)\n    at #handleOnExit (node:child_process:520:72)\n    at processTicksAndRejections (native:7:39)","timestamp":"2026-02-02T11:39:08.559Z"},{"error":"RipgrepTimeoutError: Ripgrep search timed out after 20 seconds. The search may have matched files but did not complete in time. Try searching a more specific path or pattern.\n    at D (/$bunfs/root/claude:73:189)\n    at <anonymous> (/$bunfs/root/claude:73:403)\n    at exitHandler (node:child_process:109:27)\n    at emit (node:events:98:22)\n    at #maybeClose (node:child_process:766:16)\n    at #handleOnExit (node:child_process:520:72)\n    at processTicksAndRejections (native:7:39)","timestamp":"2026-02-02T11:39:08.560Z"},{"error":"Error: Request was aborted.\n    at makeRequest (/$bunfs/root/claude:360:3940)\n    at processTicksAndRejections (native:7:39)","timestamp":"2026-02-02T12:56:50.211Z"},{"error":"MaxFileReadTokenExceededError: File content (36282 tokens) exceeds maximum allowed tokens (25000). Please use offset and limit parameters to read specific portions of the file, or use the GrepTool to search for specific content.\n    at RVB (/$bunfs/root/claude:3523:5255)\n    at async call (/$bunfs/root/claude:3532:1511)\n    at async <anonymous> (/$bunfs/root/claude:3544:1608)\n    at processTicksAndRejections (native:7:39)","timestamp":"2026-02-02T13:01:04.928Z"},{"error":"MaxFileReadTokenExceededError: File content (36282 tokens) exceeds maximum allowed tokens (25000). Please use offset and limit parameters to read specific portions of the file, or use the GrepTool to search for specific content.\n    at RVB (/$bunfs/root/claude:3523:5255)\n    at async call (/$bunfs/root/claude:3532:1511)\n    at async <anonymous> (/$bunfs/root/claude:3544:1608)\n    at processTicksAndRejections (native:7:39)","timestamp":"2026-02-02T13:01:10.038Z"},{"error":"Error: Request was aborted.\n    at i5R (/$bunfs/root/claude:1522:23441)\n    at vpB (/$bunfs/root/claude:4717:7450)\n    at processTicksAndRejections (native:7:39)","timestamp":"2026-02-02T13:09:29.815Z"},{"error":"Error: EISDIR: illegal operation on a directory, read\n    at readFileSync (unknown)\n    at <anonymous> (/$bunfs/root/claude:12:742)\n    at yC (/$bunfs/root/claude:11:40705)\n    at readFileSync (/$bunfs/root/claude:12:701)\n    at AVB (/$bunfs/root/claude:5140:20088)\n    at call (/$bunfs/root/claude:3532:1451)\n    at call (/$bunfs/root/claude:3528:7071)\n    at KD8 (/$bunfs/root/claude:3059:12903)\n    at processTicksAndRejections (native:7:39)","timestamp":"2026-02-02T13:10:42.800Z"},{"error":"Error: EISDIR: illegal operation on a directory, read\n    at readFileSync (unknown)\n    at <anonymous> (/$bunfs/root/claude:12:742)\n    at yC (/$bunfs/root/claude:11:40705)\n   …

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